One use for optical scanners is to detect fluorescence that is emitted from a sample that has been excited by a laser excitation signal. The sample may consist of a "micro-array" of elements, typically in the shape of dots, that contain chemicals, DNA and so forth that are under study. The dots, which have diameters that are measured in microns, include fluorescent tags that emit fluorescent light in response to excitation by the laser. The amount of fluorescence emitted by a dot indicates, for example, the results of a particular chemical reaction that has taken place.
Generally, a user has little idea of the brightness of the fluorescence that will be emitted by a particular sample. Accordingly, the user does not know apriori how high or low to set the attenuation of an attenuator that controls the optical excitation signal power, that is, the signal power that reaches the sample. Further, the user does not know how high or low to set the gain of a detector that collects the emitted fluorescence and produces a corresponding data signal. If the excitation signal power and/or detector gain are set too high, the system saturates, and thus, fails to make accurate measurements. If the excitation power and/or gain are set too low, the system may not accurately distinguish between different lower levels of emitted fluorescence.
In certain known prior systems, the sensitivity of the system is set by the user, who manually adjusts both the gain of the fluorescence detector and the level of attenuation of the attenuator. Typically, the user scans the sample in raster fashion, to locate an element in the micro-array that is known to contain a concentration of a fluorophor that should produce a maximum fluorescence in response to the excitation signal. The user then re-scans the portion of the sample that contains this element and iteratively adjusts the sensitivity of the system until, in the judgment of the user, the corresponding data signal is sufficiently close to a maximum data signal value of the system. If the system has two channels, that is, produces excitation signals using two lasers of different wavelengths, the user re-scans the sample using as the excitation signal the signal produced by the second laser and repeats the iterative, manual adjustment process to determine the appropriate sensitivity settings for the second channel. Similarly, the user further re-scans the sample for each additional channel.
The adjustment ranges of the attenuator and the detector are relatively large. Accordingly, manual adjustment of these components is time consuming, particularly since adjustment of either one of them may require a re-adjustment of the other. The sample may thus be scanned many times to set the sensitivity of, or calibrate, the system. When multiple channels are used, more time is spent manually calibrating the system and the sample is scanned even more times, as discussed above.
The scanning and re-scanning of the sample may damage the sample. For instance, repeated exposure to the laser signal power may cause "photo-bleaching," which results in a weakening of the fluorescence emitted in response to subsequent excitation. This means that the data collection operations may be adversely affected, particularly with respect to sample elements that produce low levels of fluorescence. The risk of damage to the sample is further increased when multiple channels are used.